Questions raised at a municipal subcommittee meeting in May triggered an audit of Pasadena’s Underground Utility Program (UUP). On Tuesday, the city released a report by the auditing firm KPMG that found $6.4 million missing while investigators from the Los Angeles County District Attorney’s office arrested three suspects.

Danny R. Wooten, a preacher and a former analyst with the city’s Department of Public Works, was charged in a 60-count felony indictment that also included Tyrone Collins and Melody Jenkins. They are charged with grand theft, embezzlement and conflict of interest. The theft was alleged to have occurred over 11 years.

City Manager Michael J. Beck called it “a complete breakdown of our internal controls.” City Councilman Terry Tornek, a critic of the UUP and a member of the committee in May where questions were first raised, said at the meeting, “I call it a slush fund because that’s what it is and I object to it.” He is running for mayor in the March 2015 election.

Wooten managed the underground program, which gets its money from a tax funded by electric customers, and allegedly fabricated 300 invoices, generating 189 checks to four fake vendors.

Wooten allegedly directed $2.8 million to Pasadena-based Southern California Evangelist Jurisdiction Center and New Covenant Christian Fellowship Foursquare Church in Pomona, where he is the senior pastor. Wooten sits on the board of the Jurisdiction Center.

More than $3.5 million was said to be directed to Altadena-based Collins Electric, owned by one of the accused, from where it was redirected to New Covenant.

Jenkins, the third person indicted, was accused of accepting $40,000 as Wooten’s personal assistant.

No funds have been recovered. The audit, which said Wooten diverted money to his own accounts, left it unclear whether the churches ever used any of the windfall.

Wooten, who worked 12 years for the city, was fired in July for what has been called an unrelated personnel matter. He is being held on $1.75-million bail.